@jbrowse/plugin-data-management 2.8.0 → 2.10.0

package/dist/ucsc-trackhub/ucscTrackHub.d.ts

@@ -1,10 +1,10 @@
-import { TrackDbFile } from '@gmod/ucsc-hub';
 import { FileLocation } from '@jbrowse/core/util';
-export declare function fetchHubFile(hubLocation: FileLocation): Promise<import("@gmod/ucsc-hub").HubFile>;
-export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<import("@gmod/ucsc-hub").GenomesFile>;
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
 export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
 export declare function makeLoc(first: string, base: {
     uri: string;
+    baseUri?: string;
 }): {
     uri: string;
     locationType: string;
@@ -19,5 +19,162 @@ export declare function makeLoc2(first: string, alt?: string): {
     uri: string | undefined;
     locationType: string;
 };
-export declare function generateTracks(trackDb: TrackDbFile, trackDbLoc: FileLocation, assemblyName: string, sequenceAdapter: any): any;
+export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }: {
+    trackDb: TrackDbFile;
+    trackDbLoc: FileLocation;
+    assemblyName: string;
+    sequenceAdapter: any;
+}): ({
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[] | undefined;
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        bamLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        index: {
+            location: {
+                uri: string | undefined;
+                locationType: string;
+            };
+        };
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        cramLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        craiLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        sequenceAdapter: any;
+        bamLocation?: undefined;
+        index?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        bigBedLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        bigWigLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        vcfGzLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        index: {
+            location: {
+                uri: string | undefined;
+                locationType: string;
+            };
+        };
+        bamLocation?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        hicLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+    };
+})[];
 export { default as ucscAssemblies } from './ucscAssemblies';

package/dist/ucsc-trackhub/ucscTrackHub.js

@@ -1,61 +1,27 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ucscAssemblies = exports.generateTracks = exports.makeLoc2 = exports.makeLocAlt = exports.makeLoc = exports.fetchTrackDbFile = exports.fetchGenomesFile = exports.fetchHubFile = void 0;
+exports.ucscAssemblies = exports.generateTracks = exports.makeLoc2 = exports.makeLocAlt = exports.makeLoc = exports.fetchTrackDbFile = exports.fetchGenomesFile = void 0;
+/* eslint-disable @typescript-eslint/no-explicit-any */
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-async function fetchHubFile(hubLocation) {
-    try {
-        const hubFileText = await (0, io_1.openLocation)(hubLocation).readFile('utf8');
-        const { HubFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
-        return new HubFile(hubFileText);
-    }
-    catch (error) {
-        throw new Error(`Not a valid hub.txt file, got error: '${error}'`);
-    }
-}
-exports.fetchHubFile = fetchHubFile;
+const ucsc_hub_1 = require("@gmod/ucsc-hub");
 async function fetchGenomesFile(genomesLoc) {
     const genomesFileText = await (0, io_1.openLocation)(genomesLoc).readFile('utf8');
-    const { GenomesFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
-    return new GenomesFile(genomesFileText);
+    return new ucsc_hub_1.GenomesFile(genomesFileText);
 }
 exports.fetchGenomesFile = fetchGenomesFile;
 async function fetchTrackDbFile(trackDbLoc) {
     const text = await (0, io_1.openLocation)(trackDbLoc).readFile('utf8');
-    const { TrackDbFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
-    return new TrackDbFile(text);
+    return new ucsc_hub_1.TrackDbFile(text);
 }
 exports.fetchTrackDbFile = fetchTrackDbFile;
 function makeLoc(first, base) {
     return {
-        uri: new URL(first, base.uri).href,
+        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
         locationType: 'UriLocation',
     };
 }
@@ -76,11 +42,11 @@ function makeLoc2(first, alt) {
         };
 }
 exports.makeLoc2 = makeLoc2;
-function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapter) {
-    var _a;
-    const tracks = [];
-    for (const [trackName, track] of trackDb.entries()) {
-        const trackKeys = [...track.keys()];
+function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }) {
+    return Object.entries(trackDb.data)
+        .map(([trackName, track]) => {
+        var _a;
+        const trackKeys = Object.keys(track);
         const parentTrackKeys = new Set([
             'superTrack',
             'compositeTrack',
@@ -88,42 +54,45 @@ function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapter) {
             'view',
         ]);
         if (trackKeys.some(key => parentTrackKeys.has(key))) {
-            continue;
+            return undefined;
         }
         const parentTracks = [];
         let currentTrackName = trackName;
         do {
-            currentTrackName = ((_a = trackDb.get(currentTrackName)) === null || _a === void 0 ? void 0 : _a.get('parent')) || '';
+            currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
             if (currentTrackName) {
                 ;
                 [currentTrackName] = currentTrackName.split(' ');
-                parentTracks.push(trackDb.get(currentTrackName));
+                parentTracks.push(trackDb.data[currentTrackName]);
             }
         } while (currentTrackName);
         parentTracks.reverse();
         const categories = parentTracks
-            .map(p => p === null || p === void 0 ? void 0 : p.get('shortLabel'))
+            .map(p => p === null || p === void 0 ? void 0 : p.data.shortLabel)
             .filter((f) => !!f);
-        const res = makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter);
-        tracks.push({
+        const res = makeTrackConfig({
+            track: track,
+            categories,
+            trackDbLoc,
+            trackDb,
+            sequenceAdapter,
+        });
+        return {
             ...res,
             trackId: `ucsc-trackhub-${(0, util_1.objectHash)(res)}`,
             assemblyNames: [assemblyName],
-        });
-    }
-    return tracks;
+        };
+    })
+        .filter(util_1.notEmpty);
 }
 exports.generateTracks = generateTracks;
-function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter) {
+function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapter, }) {
     var _a;
-    let trackType = track.get('type');
-    const name = track.get('shortLabel') || '';
-    const bigDataUrl = track.get('bigDataUrl') || '';
-    const bigDataIdx = track.get('bigDataIndex') || '';
+    const trackType = track.data.type || ((_a = trackDb.data[track.data.parent || '']) === null || _a === void 0 ? void 0 : _a.data.type) || '';
+    const name = track.data.shortLabel || '';
+    const bigDataUrl = track.data.bigDataUrl || '';
+    const bigDataIdx = track.data.bigDataIndex || '';
     const isUri = (0, util_1.isUriLocation)(trackDbLoc);
-    if (!trackType) {
-        trackType = (_a = trackDb.get(track.get('parent') || '')) === null || _a === void 0 ? void 0 : _a.get('type');
-    }
     let baseTrackType = (trackType === null || trackType === void 0 ? void 0 : trackType.split(' ')[0]) || '';
     if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
         baseTrackType = 'cram';
@@ -135,8 +104,8 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
         case 'bam':
             return {
                 type: 'AlignmentsTrack',
-                name: track.get('shortLabel'),
-                description: track.get('longLabel'),
+                name: track.data.longLabel,
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'BamAdapter',
@@ -148,142 +117,55 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
                     },
                 },
             };
-        case 'bigBarChart':
+        case 'cram':
             return {
-                type: 'FeatureTrack',
+                type: 'AlignmentsTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
+                    type: 'CramAdapter',
+                    cramLocation: bigDataLocation,
+                    craiLocation: isUri
+                        ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
+                        : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
+                    sequenceAdapter,
                 },
             };
+        case 'bigBarChart':
         case 'bigBed':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
         case 'bigGenePred':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
         case 'bigChain':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
-            };
         case 'bigInteract':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
-            };
         case 'bigMaf':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
-            };
+        case 'bigNarrowPeak':
         case 'bigPsl':
             return {
                 type: 'FeatureTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'BigBedAdapter',
                     bigBedLocation: bigDataLocation,
                 },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
             };
         case 'bigWig':
             return {
                 type: 'QuantitativeTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'BigWigAdapter',
                     bigWigLocation: bigDataLocation,
                 },
             };
-        case 'cram':
-            return {
-                type: 'AlignmentsTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'CramAdapter',
-                    cramLocation: bigDataLocation,
-                    craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
-                        : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
-                    sequenceAdapter,
-                },
-            };
-        case 'bigNarrowPeak':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
-        case 'peptideMapping':
-            return (0, tracks_1.generateUnsupportedTrackConf)(name, baseTrackType, categories);
         case 'vcfTabix':
             return {
                 type: 'VariantTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'VcfTabixAdapter',
@@ -299,7 +181,7 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
             return {
                 type: 'HicTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'HicAdapter',
@@ -307,6 +189,7 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
                 },
             };
         // unsupported types
+        //     case 'peptideMapping':
         //     case 'gvf':
         //     case 'ld2':
         //     case 'narrowPeak':

package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -94,9 +94,6 @@ const DefaultAddTrackWorkflow = observer(function ({ model, }) {
                 };
                 jobsManager.queueJob(newEntry);
             }
-            else {
-                session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
-            }
             model.clearData();
             if (isSessionModelWithWidgets(session)) {
                 session.hideWidget(model);
@@ -106,10 +103,6 @@ const DefaultAddTrackWorkflow = observer(function ({ model, }) {
             setTrackErrorMessage('Failed to add track.\nThe configuration of this file is not currently supported.');
         }
     }
-    function handleBack() {
-        setTrackErrorMessage(undefined);
-        setActiveStep(activeStep - 1);
-    }
     function isNextDisabled() {
         switch (activeStep) {
             case 0:
@@ -126,7 +119,10 @@ const DefaultAddTrackWorkflow = observer(function ({ model, }) {
             React.createElement(StepContent, null,
                 getStepContent(idx),
                 React.createElement("div", { className: classes.actionsContainer },
-                    React.createElement(Button, { disabled: activeStep === 0, onClick: handleBack, className: classes.button }, "Back"),
+                    React.createElement(Button, { disabled: activeStep === 0, onClick: () => {
+                            setTrackErrorMessage(undefined);
+                            setActiveStep(activeStep - 1);
+                        }, className: classes.button }, "Back"),
                     React.createElement(Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: handleNext, className: classes.button, "data-testid": "addTrackNextButton" }, activeStep === steps.length - 1 ? 'Add' : 'Next')),
                 trackErrorMessage ? (React.createElement("div", { className: classes.alertContainer },
                     React.createElement(Alert, { severity: "error" }, trackErrorMessage))) : null)))))));

package/esm/AddTrackWidget/model.d.ts

@@ -5,9 +5,21 @@ interface IndexingAttr {
     attributes: string[];
     exclude: string[];
 }
+/**
+ * #stateModel AddTrackModel
+ */
 export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
     type: import("mobx-state-tree").ISimpleType<"AddTrackWidget">;
+    /**
+     * #property
+     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     trackSource: string;
@@ -20,30 +32,99 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     textIndexTrack: boolean;
     textIndexingConf: IndexingAttr | undefined;
 } & {
+    /**
+     * #action
+     */
     setAdapterHint(obj: string): void;
+    /**
+     * #action
+     */
     setTrackSource(str: string): void;
+    /**
+     * #action
+     */
     setTextIndexingConf(conf: IndexingAttr): void;
+    /**
+     * #action
+     */
     setTextIndexTrack(flag: boolean): void;
+    /**
+     * #action
+     */
     setTrackData(obj: FileLocation): void;
+    /**
+     * #action
+     */
     setIndexTrackData(obj: FileLocation): void;
+    /**
+     * #action
+     */
     setAssembly(str: string): void;
+    /**
+     * #action
+     */
     setTrackName(str: string): void;
+    /**
+     * #action
+     */
     setTrackType(str: string): void;
+    /**
+     * #action
+     */
     clearData(): void;
 } & {
+    /**
+     * #getter
+     */
     readonly trackAdapter: import("@jbrowse/core/util/tracks").AdapterConfig | undefined;
+    /**
+     * #getter
+     */
     readonly trackName: string;
+    /**
+     * #getter
+     */
     readonly isFtp: boolean;
+    /**
+     * #getter
+     */
     readonly isRelativeTrackUrl: boolean;
+    /**
+     * #getter
+     */
     readonly isRelativeIndexUrl: boolean;
+    /**
+     * #getter
+     */
     readonly isRelativeUrl: boolean;
+    /**
+     * #getter
+     */
     readonly trackHttp: any;
+    /**
+     * #getter
+     */
     readonly indexHttp: any;
+    /**
+     * #getter
+     */
     readonly wrongProtocol: any;
+    /**
+     * #getter
+     */
     readonly unsupported: boolean;
+    /**
+     * #getter
+     */
     readonly assembly: any;
+    /**
+     * #getter
+     */
     readonly trackType: string;
 } & {
+    /**
+     * #getter
+     */
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type AddTrackStateModel = ReturnType<typeof f>;